The BeWiser Ducati rider held off competition from his team-mate Scott Redding – who secured the hat-trick at Donington Park in the previous round – and Tommy Bridewell, who finished second by 0.238seconds.
Brookes led from start to finish and initially was under pressure from Redding before Bridewell found a gap past the former MotoGP rider.
It means Bridewell, the Oxford Racing Ducati rider, tops the standings with 145 points, 14 ahead of Redding and 21 ahead of Brookes.
The Australian, however, could clinch a £75,000 prize if he wins all the races at Brands Hatch, Knockhill and Snetterton.
Brookes powered to victory in Race 1 at Brands Hatch in the first race of the new BSB Triple Crown.
He started second on the grid behind Redding but the start of the race saw drama as the latter began terribly, dropping way down the grid due to a poor tyre selection.
That allowed Tommy Bridewell and Dan Linfoot to take advantage as they moved into the top positions and took control of the race.
Brookes clinches third win of season in Race 1
Bridewell looked set to secure victory but right at the end things fell apart a bit as Brookes powered through the rest of the pack to take victory.
It was a hugely impressive display from Australian Brookes, who takes the win in the first of the BSB Triple Crown, a new event comprising of two races at Brands Hatch, Knockhill and Snetterton.
Bridewell had to eventually settle for third with Linfoot in second.